Merge branch 'master' of github.com:stemangiola/HCAquery

Author: stemangiola

.Rbuildignore

@@ -1,3 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^dev
+^\.github$
+^LICENSE\.md$
+^README\.Rmd$

.github/workflows/check-bioc.yml

@@ -81,36 +81,40 @@ jobs:
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
+      
+      - name: Cache assay data
+        uses: actions/cache@v3
+        with:
+          key: ${{ runner.os }}-hca-harmonised
+          path: ~/.cache/hca_harmonised
 
       - name: Cache R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v2
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -149,7 +153,7 @@ jobs:
       - name: Install BiocManager
         run: |
           message(paste('****', Sys.time(), 'installing BiocManager ****'))
-          remotes::install_cran("BiocManager")
+          remotes::install_github("Bioconductor/BiocManager")
         shell: Rscript {0}
 
       - name: Set BiocVersion
@@ -270,7 +274,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v2
         with:
           name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
           path: check

.gitignore

@@ -9,3 +9,4 @@ HCAquery.Rproj
 split_files.makeflow
 ._*
 .DS_Store
+inst/doc

DESCRIPTION

@@ -5,47 +5,67 @@ Version: 0.1.0
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre"))
                   )
-Description: Queries the Human Cell Atlas.
+Description: Provides access to a copy of the Human Cell Atlas, but with 
+    harmonised metadata. This allows for uniform querying across numerous 
+    datasets within the Atlas using common fields such as cell type, tissue 
+    type, and patient ethnicity. Usage involves first querying the metadata
+    table for cells of interest, and then downloading the corresponding cells 
+    into a SingleCellExperiment object. 
 License: GPL-3
 Depends:
-    R (>= 4.1.0)
+    R (>= 4.2.0)
 Imports:
-	dplyr,
-	SummarizedExperiment,
-	SingleCellExperiment,
-	tidySingleCellExperiment,
-	purrr,
-	zellkonverter,
-	BiocGenerics,
-	glue,
-	HDF5Array,
-	DBI,
-	RSQLite,
-	dbplyr
+    dplyr,
+    SummarizedExperiment,
+    SingleCellExperiment,
+    purrr (>= 1.0.0),
+    BiocGenerics,
+    glue,
+    HDF5Array,
+    DBI,
+    RSQLite,
+    rappdirs,
+    httr,
+    cli,
+    assertthat,
+    SeuratObject,
+    Seurat,
+    methods,
+    rlang,
+    stats,
+    RPostgres
 Suggests:
     here,
     stringr,
-    Seurat,
     tidyseurat,
+    zellkonverter,
     scMerge,
     DelayedArray,
     openssl,
     cellxgenedp,
-    SingleCellExperiment,
     celldex,
     SingleR,
     tools,
     rmarkdown,
-    SeuratObject
-VignetteBuilder:
-    knitr
-RdMacros:
-    lifecycle
+    knitr,
+    testthat,
+    dbplyr (>= 2.3.0)
 Biarch: true
-biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, Transcription, Transcriptomics
+biocViews: 
+    AssayDomain,
+    Infrastructure,
+    RNASeq,
+    DifferentialExpression,
+    GeneExpression,
+    Normalization,
+    Clustering,
+    QualityControl,
+    Sequencing,
+    Transcription,
+    Transcriptomics
 Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 LazyDataCompression: xz
 URL: https://github.com/stemangiola/HCAquery
 BugReports: https://github.com/stemangiola/HCAquery/issues
+VignetteBuilder: knitr